Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate BWI76_RS20510 BWI76_RS20510 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Koxy:BWI76_RS20510 Length = 321 Score = 598 bits (1542), Expect = e-176 Identities = 290/321 (90%), Positives = 306/321 (95%) Query: 1 MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC 60 MTK+ALVGDVGGTNARLALCD+ SGEIS+AKTYSGLDYPSLEAV++VYLEEH V+V+DGC Sbjct: 1 MTKFALVGDVGGTNARLALCDLTSGEISRAKTYSGLDYPSLEAVVQVYLEEHNVQVEDGC 60 Query: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLK EHLIQFG Sbjct: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKAEHLIQFG 120 Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 GA+PVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEE IILE LR E Sbjct: 121 GAKPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEGIILEELRTE 180 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 +GHVSAERVLSGPGLVNLY AIVK+D RLPENL+PKD+TERALAD+C DCRRALSLFCVI Sbjct: 181 LGHVSAERVLSGPGLVNLYHAIVKSDGRLPENLQPKDVTERALADTCIDCRRALSLFCVI 240 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 MGRFGGNLAL LGTFGGV+IAGGIVPRFLEFFKASGFR FEDKGRFK +V DIPVYLIV Sbjct: 241 MGRFGGNLALTLGTFGGVYIAGGIVPRFLEFFKASGFRGGFEDKGRFKAFVQDIPVYLIV 300 Query: 301 HDNPGLLGSGAHLRQTLGHIL 321 HDNPGLLGSGAHLRQTLG +L Sbjct: 301 HDNPGLLGSGAHLRQTLGQVL 321 Lambda K H 0.322 0.141 0.426 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 503 Number of extensions: 8 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS20510 BWI76_RS20510 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00749.hmm # target sequence database: /tmp/gapView.15939.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00749 [M=315] Accession: TIGR00749 Description: glk: glucokinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-153 494.0 0.0 1e-152 493.9 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS20510 BWI76_RS20510 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS20510 BWI76_RS20510 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 493.9 0.0 1e-152 1e-152 1 315 [] 6 310 .. 6 310 .. 1.00 Alignments for each domain: == domain 1 score: 493.9 bits; conditional E-value: 1e-152 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvr 71 lvgd+GGtnarlal++ ++gei+ +ktys++d+psleavv+vylee++v+++d gc+aia+Pi+gd+v+ lcl|FitnessBrowser__Koxy:BWI76_RS20510 6 LVGDVGGTNARLALCDLTSGEISRAKTYSGLDYPSLEAVVQVYLEEHNVQVED---GCIAIACPITGDWVA 73 89***************************************************...*************** PP TIGR00749 72 ltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatl 142 +tn++Wa+si+e+k++l++++le+indf+av++ai++lk e+liq+ggak++e+++ia++GaGtGlGva+l lcl|FitnessBrowser__Koxy:BWI76_RS20510 74 MTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKAEHLIQFGGAKPVEGKPIAVYGAGTGLGVAHL 144 *********************************************************************** PP TIGR00749 143 iqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevskl 213 ++ +d+r+++l+geGghvdfaP+se+e ++le lr+++g+vsaervlsG+Glv++y+a++k + +l lcl|FitnessBrowser__Koxy:BWI76_RS20510 145 VH-VDKRWVSLPGEGGHVDFAPNSEEEGIILEELRTELGHVSAERVLSGPGLVNLYHAIVKSD-----GRL 209 **.************************************************************.....89* PP TIGR00749 214 skeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfra 284 + e+l++kd++e+al++++ ++rral+lf++i+G+++gnlal+lg++GGvy+aGGivPrf+e++k+s+fr lcl|FitnessBrowser__Koxy:BWI76_RS20510 210 P-ENLQPKDVTERALADTCIDCRRALSLFCVIMGRFGGNLALTLGTFGGVYIAGGIVPRFLEFFKASGFRG 279 *.9******************************************************************** PP TIGR00749 285 afedkGrlkellasiPvqvvlkkkvGllGag 315 +fedkGr+k+++++iPv++++++++GllG+g lcl|FitnessBrowser__Koxy:BWI76_RS20510 280 GFEDKGRFKAFVQDIPVYLIVHDNPGLLGSG 310 *****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (321 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.84 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory